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How can I use TCGA Copy Number Portal?

I have a list of 500 genes of my interest in a certain cancer type.

I would like to know if these genes are significantly amplified/loss or not respectively.

Is there any way to collect the CNV analysis result (such as q-value) for the 500 genes from TCGA CN portal (http://www.broadinstitute.org/tcga/home) ?

I read FAQ and help in TCGA CN portal, but I still don't know the way.

Also, I sent this question to the support e-mail address (tcga-help[at]broadinstitute.org), but it was rejected by the server.

I also knows there is GDAC Firehose pipeline though, I would like to use the TCGA CN portal pipeline.

tcga cnv
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updated by raunakms raunakms • written by nijironohata • nijironohata

1 answer

Use CBioPortal: http://www.cbioportal.org/ is you just want a quick check for your genes of interest,

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written by raunakms raunakms

I think cBio don't respond if each gene of my interest is significantly amplified/loss or not with p-value (or q-value). I want the result with statistic value. Thank you for your comment.

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written by nijironohata • nijironohata

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